Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Sequencing quality”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 343 records · Page 19Linked to original sources
PubMed2006

MamPol: a database of nucleotide polymorphism in the Mammalia class.

Multi-locus and multi-species nucleotide diversity studies would benefit enormously from a public database encompassing high-quality haplotypic sequences with their associated genetic diversity measures. MamPol, 'Mammalia Polymorphism Database', is a website containing all the well-annotated polymorphic sequences available in GenBank for the Mammalia class grouped by name of organism and gene. Diversity measures of single nucleotide polymorphisms are provided for each set of haplotypic homologous sequences, including polymorphism at synonymous and non-synonymous sites, linkage disequilibrium and codon bias. Data gathering, calculation of diversity measures and daily updates are automatically performed using PDA software. The MamPol website includes several interfaces for browsing the contents of the database and making customizable comparative searches of different species or taxonomic groups. It also contains a set of tools for simple re-analysis of the available data and a statistics section that is updated daily and summarizes the contents of the database. MamPol is available at http://mampol.uab.es/ and can be downloaded via FTP.

Animals↗
PubMed2005

Whole-body magnetic resonance imaging.

Whole-body magnetic resonance imaging is a fast and accurate modality for the detection of disease throughout the entire body. Technical improvements including the availability of different high image quality MR sequences, the remote movement of the imaging table, and the use of specialized surface coils have rendered whole-body screening with MRI a feasible method. In this article we describe underlying techniques and report on first clinical experiences of whole-body magnetic resonance imaging as a staging and screening method. Furthermore, advantages and limitations compared with whole-body imaging based on computed tomography are discussed.

Contrast Media↗
PubMed2025

Global diversity of integrating conjugative elements (ICEs) in Helicobacter pylori and their influence on genome architecture.

Integrating conjugative elements (ICEs) are mobile genetic elements conferring a wide range of beneficial functions upon their bacterial hosts. Generally, they can be activated from their integrated states to undergo horizontal gene transfer via conjugation. In the case of the human gastric pathogen Helicobacter pylori, a paradigm for extensive genetic diversity, highly efficient natural transformation and recombination processes may superimpose canonical transfer of its two ICEs termed ICEHptfs3 and ICEHptfs4, and thus shape their composition substantially. Here, as a part of the Helicobacter pylori Genome Project (HpGP) initiative, we have analyzed high-quality genome sequences from 1011 clinical strains with respect to their ICE content and variability. We show that both elements are highly prevalent in all H. pylori populations, but have a strong tendency for gene erosion. ICE sequence variations reflect the population structure and show a clear signature of increased horizontal transfer. A detailed map of ICE integration sites revealed local preferences, but also how recombination processes result in hybrid elements or genome rearrangements. Population-specific differences in ICE cargo genes might reflect distinct requirements in the biological functions provided by these mobile elements.

Journal Article↗
PubMed2004

Characterization of the maize endosperm transcriptome and its comparison to the rice genome.

The cereal endosperm is a major organ of the seed and an important component of the world's food supply. To understand the development and physiology of the endosperm of cereal seeds, we focused on the identification of genes expressed at various times during maize endosperm development. We constructed several cDNA libraries to identify full-length clones and subjected them to a twofold enrichment. A total of 23,348 high-quality sequence-reads from 5'- and 3'-ends of cDNAs were generated and assembled into a unigene set representing 5326 genes with paired sequence-reads. Additional sequencing yielded a total of 3160 (59%) completely sequenced, full-length cDNAs. From 5326 unigenes, 4139 (78%) can be aligned with 5367 predicted rice genes and by taking only the "best hit" be mapped to 3108 positions on the rice genome. The 22% unigenes not present in rice indicate a rapid change of gene content between rice and maize in only 50 million years. Differences in rice and maize gene numbers also suggest that maize has lost a large number of duplicated genes following tetraploidization. The larger number of gene copies in rice suggests that as many as 30% of its genes arose from gene amplification, which would extrapolate to a significant proportion of the estimated 44,027 candidate genes of its entire genome. Functional classification of the maize endosperm unigene set indicated that more than a fourth of the novel functionally assignable genes found in this study are involved in carbohydrate metabolism, consistent with its role as a storage organ.

DNA, Complementary↗
PubMed2005

Assembly of polymorphic genomes: algorithms and application to Ciona savignyi.

Whole-genome assembly is now used routinely to obtain high-quality draft sequence for the genomes of species with low levels of polymorphism. However, genome assembly remains extremely challenging for highly polymorphic species. The difficulty arises because two divergent haplotypes are sequenced together, making it difficult to distinguish alleles at the same locus from paralogs at different loci. We present here a method for assembling highly polymorphic diploid genomes that involves assembling the two haplotypes separately and then merging them to obtain a reference sequence. Our method was developed to assemble the genome of the sea squirt Ciona savignyi, which was sequenced to a depth of 12.7 x from a single wild individual. By comparing finished clones of the two haplotypes we determined that the sequenced individual had an extremely high heterozygosity rate, averaging 4.6% with significant regional variation and rearrangements at all physical scales. Applied to these data, our method produced a reference assembly covering 157 Mb, with N50 contig and scaffold sizes of 47 kb and 989 kb, respectively. Alignment of ESTs indicates that 88% of loci are present at least once and 81% exactly once in the reference assembly. Our method represented loci in a single copy more reliably and achieved greater contiguity than a conventional whole-genome assembly method.

Algorithms↗
PubMed2005

The canine genome.

The dog has emerged as a premier species for the study of morphology, behavior, and disease. The recent availability of a high-quality draft sequence lifts the dog system to a new threshold. We provide a primer to use the dog genome by first focusing on its evolutionary history. We overview the relationship of dogs to wild canids and discuss their origin and domestication. Dogs clearly originated from a substantial number of gray wolves and dog breeds define distinct genetic units that can be divided into at least four hierarchical groupings. We review evidence showing that dogs have high levels of linkage disequilibrium. Consequently, given that dog breeds express specific phenotypic traits and vary in behavior and the incidence of genetic disease, genomic-wide scans for linkage disequilibrium may allow the discovery of genes influencing breed-specific characteristics. Finally, we review studies that have utilized the dog to understand the genetic underpinning of several traits, and we summarize genomic resources that can be used to advance such studies. We suggest that given these resources and the unique characteristics of breeds, that the dog is a uniquely valuable resource for studying the genetic basis of complex traits.

Animals↗
PubMed1999

Nutritional genomics: manipulating plant micronutrients to improve human health.

The nutritional health and well-being of humans are entirely dependent on plant foods either directly or indirectly when plants are consumed by animals. Plant foods provide almost all essential vitamins and minerals and a number of other health-promoting phytochemicals. Because micronutrient concentrations are often low in staple crops, research is under way to understand and manipulate synthesis of micronutrients in order to improve crop nutritional quality. Genome sequencing projects are providing novel approaches for identifying plant biosynthetic genes of nutritional importance. The term "nutritional genomics" is used to describe work at the interface of plant biochemistry, genomics, and human nutrition.

Computational Biology↗
PubMed1987

Detection of colonic polyps on single-contrast barium enema study: emphasis on the elderly.

A systems approach was employed to improve results of the single-contrast barium enema examination for detection of colonic polyps. Improvements were made in each of the following areas: radiographic-fluoroscopic equipment, fluoroscopic-television images, screen-film combinations, barium suspensions, examination techniques, imaging sequences, and quality controls. Radiologic-endoscopic correlation was undertaken for 137 colonic polyps seen endoscopically in 91 patients. The average age of the patients was 69 years. The sensitivity of the single-contrast examination for detection of all polyps was 80%. Polyps 5-9 mm in size were detected with 66% sensitivity, while 94% of polyps 10 mm or larger were detected. The results indicate that the sensitivity of a suitably performed single-contrast barium enema examination may approach that of the double-contrast study for the detection of colonic polyps, even in an elderly and infirm patient population.

Adult↗
PubMed1990

Plaque fluid as a bacterial milieu.

Studies of the extracellular, free concentrations of substrates, growth factors, inhibitors, and end-products of metabolism to which the intact plaque microflora is exposed in situ can assist in the understanding of factors controlling plaque pathogenicity. Information is becoming increasingly available from analysis of fluid separated by centrifugation of plaques collected at various intervals after an intra-oral pulse of dietary or experimental substrate, or different procedures or treatments having cariostatic potential. Such analytical results give more information than those obtained by analysis of aqueous or other extracts, because they yield values of substrate concentration representing those occurring at the bacterial cell surface. The largest body of information concerns extracellular levels of acid end-products of sugar catabolism in relation to food quality or sequence, and of amino acids and other products of nitrogen metabolism, in relation to studies of the detailed metabolic events of the Stephan curve, and of the demineralizing effect of the plaque environment. Areas where little information is available and which merit further study include plaque clearance of salivary and other components with anti-caries activity (e.g., antibodies, enzymes, fluorides, cations, other antimicrobials, etc.), and substrate concentrations to determine gradients for diffusion into and out of plaque.

Amino Acids↗
PubMed2002

Correct positioning of the venous port-a-cath catheter: comparison of intravascular electrocardiography signal from guidewire and sodium bicarbonate flushed catheter.

A prospective study comparing the efficacy of wire-conducted intravascular ECG (IVECG) signal and signal from the port with a sodium bicarbonate (NaHCO3) flushed catheter to correctly place a catheter tip was carried out in 100 patients. The correct position of the catheter tip was confirmed as follows: with technique G, the IVECG signal was conducted from a guide wire to identify the tip position. With technique P, the IVECG signal was conducted from the port with a NaHCO3 (0.8 mmol/ml) flushed catheter to ascertain the tip position. Each patient received both technique G and technique P in a randomized sequence. The quality of IV-ECG signals, which included baseline drift, P wave pattern and QRS wave pattern, were assessed for ten seconds. Satisfactory quality of these IVECG signals was observed in all of the patients with technique P and 90 of the 100 patients with technique G, and this difference was significant (P=0.001). There was no obvious difference between the techniques in catheter tip placement time or the measured optimal catheter length. The incidence of atrial premature contractions was higher with technique G than with technique P (13% vs 2%; P=0.003). Therefore, technique P is a practical alternative for correctly placing the catheter tip of a Port-A-Cath.

Catheterization, Central Venous↗
PubMed2006

LocustDB: a relational database for the transcriptome and biology of the migratory locust (Locusta migratoria).

BACKGROUND: The migratory locust (Locusta migratoria) is an orthopteran pest and a representative member of hemimetabolous insects for biological studies. Its transcriptomic data provide invaluable information for molecular entomology and pave a way for the comparative research of other medically, agronomically, and ecologically relevant insects. We developed the first transcriptomic database of the locust (LocustDB), building necessary infrastructures to integrate, organize, and retrieve data that are either currently available or to be acquired in the future. DESCRIPTION: LocustDB currently hosts 45,474 high-quality EST sequences from the locust, which were assembled into 12,161 unigenes. It, through user-friendly web interfaces, allows investigators to freely access sequence data, including homologous/orthologous sequences, functional annotations, and pathway analysis, based on conserved orthologous groups (COG), gene ontology (GO), protein domain (InterPro), and functional pathways (KEGG). It also provides information from comparative analysis based on data from the migratory locust and five other invertebrate species, including the silkworm, the honeybee, the fruitfly, the mosquito and the nematode. The website address of LocustDB is http://locustdb.genomics.org.cn/. CONCLUSION: LocustDB starts with the first transcriptome information for an orthopteran and hemimetabolous insect and will be extended to provide a framework for incorporating in-coming genomic data of relevant insect groups and a workbench for cross-species comparative studies.

Animals↗
PubMed2004

Reconstruction of regulatory and metabolic pathways in metal-reducing delta-proteobacteria.

BACKGROUND: Relatively little is known about the genetic basis for the unique physiology of metal-reducing genera in the delta subgroup of the proteobacteria. The recent availability of complete finished or draft-quality genome sequences for seven representatives allowed us to investigate the genetic and regulatory factors in a number of key pathways involved in the biosynthesis of building blocks and cofactors, metal-ion homeostasis, stress response, and energy metabolism using a combination of regulatory sequence detection and analysis of genomic context. RESULTS: In the genomes of delta-proteobacteria, we identified candidate binding sites for four regulators of known specificity (BirA, CooA, HrcA, sigma-32), four types of metabolite-binding riboswitches (RFN-, THI-, B12-elements and S-box), and new binding sites for the FUR, ModE, NikR, PerR, and ZUR transcription factors, as well as for the previously uncharacterized factors HcpR and LysX. After reconstruction of the corresponding metabolic pathways and regulatory interactions, we identified possible functions for a large number of previously uncharacterized genes covering a wide range of cellular functions. CONCLUSIONS: Phylogenetically diverse delta-proteobacteria appear to have homologous regulatory components. This study for the first time demonstrates the adaptability of the comparative genomic approach to de novo reconstruction of a regulatory network in a poorly studied taxonomic group of bacteria. Recent efforts in large-scale functional genomic characterization of Desulfovibrio species will provide a unique opportunity to test and expand our predictions.

Bacterial Proteins↗
PubMed2003

Transcriptome analysis of mouse stem cells and early embryos.

Understanding and harnessing cellular potency are fundamental in biology and are also critical to the future therapeutic use of stem cells. Transcriptome analysis of these pluripotent cells is a first step towards such goals. Starting with sources that include oocytes, blastocysts, and embryonic and adult stem cells, we obtained 249,200 high-quality EST sequences and clustered them with public sequences to produce an index of approximately 30,000 total mouse genes that includes 977 previously unidentified genes. Analysis of gene expression levels by EST frequency identifies genes that characterize preimplantation embryos, embryonic stem cells, and adult stem cells, thus providing potential markers as well as clues to the functional features of these cells. Principal component analysis identified a set of 88 genes whose average expression levels decrease from oocytes to blastocysts, stem cells, postimplantation embryos, and finally to newborn tissues. This can be a first step towards a possible definition of a molecular scale of cellular potency. The sequences and cDNA clones recovered in this work provide a comprehensive resource for genes functioning in early mouse embryos and stem cells. The nonrestricted community access to the resource can accelerate a wide range of research, particularly in reproductive and regenerative medicine.

Animals↗
PubMed2003

Advanced life support therapy on out-of-hospital cardiac arrest patients: an engineering perspective.

In the USA alone, several hundred thousand people die of sudden cardiac arrests each year. Basic life support, defined as chest compressions and ventilations, and early defibrillation are the only factors proven to increase the survival of patients with out-of-hospital cardiac arrest and are key elements in the chain of survival defined by the American Heart Association. The current cardiopulmonary resuscitation guidelines treat all patients the same but studies show a need for more individualization of treatment. This review focusses on ideas on how to strengthen the weak parts of the chain of survival including the ability to measure the effects of therapy, improve time efficiency and optimize the sequence and quality of the various components of cardiopulmonary resuscitation.

Advanced Cardiac Life Support↗
PubMed2004

Cardiac cine parallel imaging on a 0.7T open system.

BACKGROUND: Parallel imaging can be applied to cardiac imaging with a cylindrical MRI (magnetic resonance imaging) apparatus. Studies of open MRI, however, are few. This study sought to achieve cardiac cine parallel imaging (or RAPID, for "rapid acquisition through parallel imaging design") with an open 0.7T MRI apparatus. MATERIALS AND METHODS: Imaging time was shortened in all slice directions with the use of a dedicated four-channel RF receiving coil comprising solenoid coils and butterfly coils. Coil shape was designed through an RF-coil simulation that considered biological load. The auto-calibration of a 0.7T open MRI apparatus incorporated a modified image-domain reconstruction algorithm. Cine images were obtained with a BASG, or balanced SARGE (steady-state acquisition with rewound gradient echo), sequence. Image quality was evaluated with cylindrical phantoms and five healthy volunteers. RESULTS: Multi-slice phantom images showed no visible artifacts. Cine images taken under breath-hold with an acceleration factor of two were evaluated carefully. With auto-calibration, the images revealed no visible unfolded artifacts or motion artifacts. RAPID thus improved the acquisition speed, time resolution, and spatial resolution of short-axis, long-axis, and four-chamber images. CONCLUSION: The use of a dedicated RF coil enabled cardiac cine RAPID to be performed with an open MRI apparatus.

Artifacts↗
PubMed1993

Solid phase purification in automated DNA sequencing.

A solid phase purification method has been utilized to investigate the effect of template DNA and other contaminants present in enzymatic DNA sequencing reactions upon data quality in automated DNA sequence analysis. The primer oligonucleotide is prepared with an internal biotin group and one of four fluorescent tags at the 5' terminus. The fluorescently labeled DNA fragments produced in the sequencing reactions are separated from other reaction components, including template DNA, using superparamagnetic streptavidin beads. Template DNA and other reaction components may then be added back to the purified material to assess their effect upon sequence data. It is found that band intensity and base calling accuracy are decreased by the presence of the template DNA and other reaction components.

Animals↗
PubMed2000

Facility management in German hospitals.

Facility management and optimum building management offer for hospitals a chance to reduce costs and to increase quality, process sequences, employee motivation and customer satisfaction. Some years ago simple services such as cleaning, catering or laundry were outsourced. Now, German hospitals progress to more complex fields such as building and medical technology, clinical support processes such as pharmacy, central laboratory and sterilization, goods and logistics services.

Cost Savings↗